Drosophila eugracilis – Akt

Gene Model for Akt in the D. eugracilis (DeugGB2) assembly (GCA_000236325.2).


Introduction
The insulin signaling pathway is a highly conserved pathway in animals, and is central to nutrient uptake (Hietakangas andCohen 2009, Grewal 2009). Akt kinase (Akt also known as Akt1, Protein Kinase B, PKB; FBgn0010379) regulates stress response, aging, and cell growth and survival in Drosophila (Stavely et al., 1998;Verdu et al., 1999). It is involved in signal transduction pathways in physiological and neurological pathways in Drosophila (Guo and Zhong 2006). It encodes a core serine-threonine kinase (Bellacosa et al. 1991) component of the Insulin-like growth factor pathway that functions downstream of, and following its activation by the Pi3K92E product in Drosophila (Andjelkovic et al., 1995). It is activated by phosphatidylinositol binding and phosphorylation (Potter et al., 2002). The gene model reported (Deug_Akt) was determined in the Apr. 2013 (BCM-HGSC/Deug_2.0; GCA_000236325.2) of D. eugracilis and compared to the ortholog dmel_Akt (GCA_000001215.4, FB2021_02; Larkin et al., 2021). D. eugracilis is part of the melanogaster species group within the subgenus Sophophora of Drosophila (Pélandakis et al., 1993). It was first described as Tanygastrella gracilis by Duda (1924) and revised to Drosophila eugracilis by Bock and Wheeler (1972). D. eugracilis is found in humid tropical and subtropical forests across southeast Asia (https://www.taxodros.uzh.ch). The methods and dataset versions used to establish the gene model are described in Rele et al. (2020). The Genomics Education Partnership maintains a mirror of the UCSC Genome Browser (Kent WJ et al., 2002;Gonzalez et al., 2021), which is available at http://gander.wustl.edu.The predicted gene model in D. eugracilis for Akt was found in NCBI RefSeq Accession XM_017228041.1 and Locus ID LOC108116251.

Protein Model
There are five RNA isoforms of Akt: Akt-RA, Akt-RB, Akt-RC, Akt-RD, and Akt-RE. The RA, RB, RD, and RE isoforms have identical protein coding sequences, represented by the Akt-PE protein isoform here. The Akt-PC coding sequence is unique.
Both the Akt-PC and Akt-PE isoforms in D. melanogaster are encoded by six coding exons. The Akt-PC and Akt-PE isoforms in D. eugracilis are encoded by six coding exons ( Figure 1B). The coordinates of the curated gene models can be found in NCBI at GenBank/BankIt using the accessions BK059589, BK059590, BK059591, BK059592, and BK059593, one for each protein-coding isoform of Akt. These data are also available in Extended Data files below, which are archived in CaltechData.

Non-canonical Start Codon:
The Akt-RC isoform has a non-canonical ACG start codon. This is well conserved across the 28 Drosophila species as shown in Figure 1D. This non-canonical start codon is used for the translation of the Akt-PC isoform in D. melanogaster, ( Figure 1D). There is a high level of conservation of the non-canonical ACG start codon (encoding threonine) across all 28 Drosophila species, as well as high conservation of the region surrounding the non-canonical start codon. This provides evidence for the existence of a non-canonical start codon in the Akt-PC isoform in D. eugracilis.

Methods
Detailed methods including algorithms, database versions, and citations for the complete annotation process can be found in Rele et al. (2020).